With an existing, pre-validated epub, I do something similar to doitsu, but I use 7zip: open the archive in 7zip (no need to rename epub to zip) and drag the xml file into the META-INF folder. Of course if the mimetype file isn't already properly first and uncompressed, it's all moot anyway.

I do not understand your last words.

I take a clean EPUB (see lower down)

Code:

Epubcheck Version 3.0
Validating against EPUB version 2.0
No errors or warnings detected.

Open it with 7-zip (1), open META-INF (2), insert the file (3),

Epubcheck is angry:

Code:

Epubcheck Version 3.0
ERROR: Brochette de cœurs v2.epub: Length of the first filename in archive must be 8, but was 45
Validating against EPUB version 2.0
Check finished with warnings or errors

Of course, why this file goes from 500k (properties) to 800k (screen 1) is another mystery...